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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic

Gene

PPOX1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). Involved in the PLP salvage pathway. Has a higher preference for PNP over PMP. May also catalyze the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S-specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX.2 Publications

Miscellaneous

Mutants with reduced expression of PPOX1 (RNAi) have lower levels of total B6 vitamers, a reduced growth and are sensitive to high light.1 Publication

Catalytic activityi

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2.2 Publications
Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.
(6R)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = (6S)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide.Curated
(6R)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = (6S)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate.Curated

Cofactori

Protein has several cofactor binding sites:
  • FMNBy similarityNote: Binds 1 FMN per subunit.By similarity
  • K+By similarityNote: Binds 1 potassium ion per subunit.By similarity

Pathwayi: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate.
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxine/pyridoxamine 5'-phosphate oxidase 2 (PPOX2), Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic (PPOX1)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Pathwayi: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate.
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxine/pyridoxamine 5'-phosphate oxidase 2 (PPOX2), Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic (PPOX1)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi132PotassiumBy similarity1
Metal bindingi196PotassiumBy similarity1
Binding sitei238NAD(P)HXBy similarity1
Metal bindingi241PotassiumBy similarity1
Binding sitei379Pyridoxal 5'-phosphateBy similarity1
Binding sitei418FMNBy similarity1
Binding sitei436Pyridoxal 5'-phosphateBy similarity1
Binding sitei440Pyridoxal 5'-phosphateBy similarity1
Binding sitei444Pyridoxal 5'-phosphateBy similarity1
Binding sitei499FMNBy similarity1
Binding sitei509FMNBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi374 – 377FMNBy similarity4
Nucleotide bindingi389 – 390FMNBy similarity2
Nucleotide bindingi395 – 396FMNBy similarity2
Nucleotide bindingi453 – 454FMNBy similarity2

GO - Molecular functioni

  • FMN binding Source: InterPro
  • metal ion binding Source: UniProtKB-KW
  • NADHX epimerase activity Source: TAIR
  • NADPHX epimerase activity Source: TAIR
  • pyridoxamine-phosphate oxidase activity Source: TAIR

GO - Biological processi

  • NADH metabolic process Source: TAIR
  • NADP metabolic process Source: TAIR
  • pyridoxine biosynthetic process Source: UniProtKB-KW

Keywordsi

Molecular functionIsomerase, Multifunctional enzyme, Oxidoreductase
Biological processPyridoxine biosynthesis
LigandFlavoprotein, FMN, Metal-binding, NAD, Nucleotide-binding, Potassium

Enzyme and pathway databases

BioCyciARA:AT5G49970-MONOMER
MetaCyc:MONOMER-17901
BRENDAi5.1.99.6 399
ReactomeiR-ATH-197264 Nicotinamide salvaging
UniPathwayiUPA01068; UER00304
UPA01068; UER00305

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic
Short name:
AtPPOX1
Including the following 2 domains:
Pyridoxine/pyridoxamine 5'-phosphate oxidase (EC:1.4.3.52 Publications)
Alternative name(s):
PNP/PMP oxidase
Short name:
PNPOx
Pyridoxal 5'-phosphate synthase
Probable NAD(P)HX epimerase (EC:5.1.99.6Curated)
Gene namesi
Name:PPOX1
Synonyms:PDX3, PDXH
Ordered Locus Names:At5g49970
ORF Names:K9P8.11
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

AraportiAT5G49970
TAIRilocus:2158814 AT5G49970

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 64ChloroplastCombined sourcesAdd BLAST64
ChainiPRO_000042054965 – 530Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplasticAdd BLAST466

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei65N-acetylmethionineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiQ9LTX3
PRIDEiQ9LTX3

PTM databases

iPTMnetiQ9LTX3

Expressioni

Tissue specificityi

Expressed in leaves, stems, flowers and roots.1 Publication

Inductioni

Circadian regulation. Up-regulated by light, heat, jasmonic acid, ethylene and abscisic acid treatments. Down-regulated by drought and salt treatment. Not induced by UV irradiation.1 Publication

Gene expression databases

ExpressionAtlasiQ9LTX3 baseline and differential
GenevisibleiQ9LTX3 AT

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi3702.AT5G49970.1

Structurei

3D structure databases

ProteinModelPortaliQ9LTX3
SMRiQ9LTX3
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini81 – 297YjeF N-terminalAdd BLAST217

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni131 – 135NAD(P)HXBy similarity5
Regioni200 – 206NAD(P)HXBy similarity7
Regioni247 – 250Pyridoxal 5'-phosphate bindingBy similarity4
Regioni321 – 324Substrate bindingBy similarity4
Regioni325 – 327Pyridoxal 5'-phosphate bindingBy similarity3
Regioni505 – 507Pyridoxal 5'-phosphate bindingBy similarity3

Domaini

Most plant PPOX proteins have both a pyridoxamine 5'-phosphate oxidase domain and an extra YjeF N-terminal domain.

Sequence similaritiesi

In the N-terminal section; belongs to the NnrE/AIBP family.Curated
In the C-terminal section; belongs to the pyridoxamine 5'-phosphate oxidase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG2585 Eukaryota
KOG2586 Eukaryota
COG0062 LUCA
COG0259 LUCA
HOGENOMiHOG000243404
KOiK00275
K17759
OMAiFWQGQKS
OrthoDBiEOG093606VO
PhylomeDBiQ9LTX3

Family and domain databases

Gene3Di2.30.110.10, 1 hit
3.40.50.10260, 1 hit
HAMAPiMF_01966 NADHX_epimerase, 1 hit
MF_01629 PdxH, 1 hit
InterProiView protein in InterPro
IPR000659 Pyridox_Oxase
IPR019740 Pyridox_Oxase_CS
IPR021198 Pyridox_Oxase_pln
IPR011576 Pyridox_Oxase_put
IPR019576 Pyridoxamine_oxidase_dimer_C
IPR012349 Split_barrel_FMN-bd
IPR004443 YjeF_N_dom
IPR036652 YjeF_N_dom_sf
PANTHERiPTHR10851:SF0 PTHR10851:SF0, 1 hit
PfamiView protein in Pfam
PF10590 PNP_phzG_C, 1 hit
PF01243 Putative_PNPOx, 1 hit
PF03853 YjeF_N, 1 hit
PIRSFiPIRSF037048 PyrdxN_5-P_Oxase_ross-cont_pln, 1 hit
SUPFAMiSSF64153 SSF64153, 1 hit
TIGRFAMsiTIGR00558 pdxH, 1 hit
TIGR00197 yjeF_nterm, 1 hit
PROSITEiView protein in PROSITE
PS01064 PYRIDOX_OXIDASE, 1 hit
PS51385 YJEF_N, 1 hit

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9LTX3-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MRNVIRRVTT MTFTFLLQSP PLPISPSPPQ FSLSSSPLSK TQRFITPSQG
60 70 80 90 100
SRLRTLCTKV IIPNMQDSGS PPLSYLTQRE AAEIDETLMG PLGFSIDQLM
110 120 130 140 150
ELAGLSVAAS IAEVYKPEEY SRVLAICGPG NNGGDGLVAA RHLHHFGYKP
160 170 180 190 200
FICYPKRTAK PLYTGLVTQL DSLSVPFVSV EDLPDDLSKD FDVIVDAMFG
210 220 230 240 250
FSFHGAPRPP FDDLIRRLVS LQNYEQTLQK HPVIVSVDIP SGWHVEEGDH
260 270 280 290 300
EDGGIKPDML VSLTAPKLCA KRFRGPHHFL GGRFVPPSVA EKYKLELPSY
310 320 330 340 350
PGTSMCVRIG KPPKVDISAM RVNYVSPELL EEQVETDPTV QFRKWFDEAV
360 370 380 390 400
AAGLRETNAM ALSTANKDKK PSSRMVLLKG FDENGFVWFT NYESKKGSDL
410 420 430 440 450
SENPSAALLF YWEILNRQVR IEGPVERIPE SESENYFHSR PRGSQIGAIV
460 470 480 490 500
SKQSSVVPGR HVLYDEYEEL TKQYSDGSVI PKPKNWGGFR LKPNLFEFWQ
510 520 530
GQPSRLHDRL QYSLQDVNGN PAWKIHRLAP
Length:530
Mass (Da):59,376
Last modified:October 1, 2000 - v1
Checksum:i22E8DFEC1A2167EE
GO
Isoform 2 (identifier: Q9LTX3-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     261-271: Missing.
     478-530: Missing.

Note: Not detected in roots.
Show »
Length:466
Mass (Da):52,042
Checksum:i3E2B851F982461E5
GO

Sequence cautioni

The sequence AAM65907 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAM83249 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti241S → Y in AAM65907 (Ref. 4) Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_044534261 – 271Missing in isoform 2. CuratedAdd BLAST11
Alternative sequenceiVSP_044535478 – 530Missing in isoform 2. CuratedAdd BLAST53

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB024032 Genomic DNA Translation: BAA97018.1
CP002688 Genomic DNA Translation: AED95878.1
CP002688 Genomic DNA Translation: AED95879.1
AY127025 mRNA Translation: AAM83249.1 Different initiation.
BT000605 mRNA Translation: AAN18174.1
AY088368 mRNA Translation: AAM65907.1 Different initiation.
RefSeqiNP_568717.2, NM_124376.4 [Q9LTX3-1]
NP_974918.1, NM_203189.2 [Q9LTX3-2]
UniGeneiAt.28155

Genome annotation databases

EnsemblPlantsiAT5G49970.1; AT5G49970.1; AT5G49970 [Q9LTX3-1]
AT5G49970.2; AT5G49970.2; AT5G49970 [Q9LTX3-2]
GeneIDi835061
GrameneiAT5G49970.1; AT5G49970.1; AT5G49970 [Q9LTX3-1]
AT5G49970.2; AT5G49970.2; AT5G49970 [Q9LTX3-2]
KEGGiath:AT5G49970

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiPPOX1_ARATH
AccessioniPrimary (citable) accession number: Q9LTX3
Secondary accession number(s): F4K7H2, Q8L7T7, Q8L9L3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 9, 2013
Last sequence update: October 1, 2000
Last modified: May 23, 2018
This is version 131 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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